edit config and readme

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'unibe_ibu', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -128,6 +128,7 @@ Currently documentation is available for the following systems:
 * [SEG_GLOBE](docs/seg_globe.md)
 * [SHH](docs/shh.md)
 * [UCT_HPC](docs/uct_hpc.md)
+* [UNIBE_IBU](docs/unibe_ibu.md)
 * [UPPMAX](docs/uppmax.md)
 * [UTD_GANYMEDE](docs/utd_ganymede.md)
 * [UZH](docs/uzh.md)

conf/unibe_ibu.config

@@ -0,0 +1,23 @@
+params {
+    config_profile_description = "University of Bern, Interfaculty Bioinformatics Unit cluster profile"
+	config_profile_contact = "irene.keller@dbmr.unibe.ch; info@bioinformatics.unibe.ch"
+	config_profile_url = "https://www.bioinformatics.unibe.ch/"
+	max_memory = 500.GB
+	max_cpus = 128
+	max_time = 28.d
+}
+
+process {
+    executor = "slurm"
+	maxRetries = 2
+	beforeScript = 'mkdir -p ./tmp/ && export TMPDIR=./tmp/'
+}
+
+executor {
+    queueSize = 30
+}
+
+singularity {
+    enable = true
+	autoMounts = true
+}

docs/unibe_ibu.md

@@ -0,0 +1,8 @@
+# nf-core/configs: UNIBE_IBU Configuration
+
+Configuration file to run nf-core pipelines on the cluster of the [Interfaculty Bioinformatics Unit](https://www.bioinformatics.unibe.ch/) of the University of Bern. 
+
+To use, run the pipeline with `-profile unibe_ibu`. This will download and launch the profile.config which has been pre-configured with a setup suitable for the IBU cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. **This requires a local installation of singularity**. It is easiest to submit the pipeline from a compute node. Once the image is cached, you can also submit from the login node.
+
+
+

nfcore_custom.config

@@ -47,6 +47,7 @@ profiles {
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
   shh          { includeConfig "${params.custom_config_base}/conf/shh.config" }
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
+  unibe_ibu    { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
   utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" }
   uzh          { includeConfig "${params.custom_config_base}/conf/uzh.config" }